A 4-bp natural deletion of maize Na+/H+ exchanger gene alters maize salt stress tolerance

• Map-based cloning a major salt tolerance QTL, qST1 , which encodes a Na + / H + exchanger transporter ZmSOS1. • In salt-sensitive maize variety D9H, the 4-bp deletion variation in ZmSOS1 coding sequence causes maize salt sensitivity and the 4-bp deletion was rarely found in the natural population but appeared in an important heterotic group composed of x1132x-derived inbred lines in China. • The 4-bp InDel marker is developed and successfully used to predict and improve maize salt tolerance. Soil salinity is a major environmental constraint severely reducing plant growth and crop productivity worldwide. Knowledge of salt tolerance-related genes can facilitate improving crop salt tolerance. Here, we identified a major locus SALT TOLERANCE 1 ( qST1 ) conferring maize salt tolerance via bulked segregant RNA-Seq. qST1 encodes a plasma membrane Na + /H + exchanger ZmSOS1, which is the ortholog of Arabidopsis thaliana SOS1 gene. In salt-sensitive variety D9H, the 4-bp deletion variation in ZmSOS1 coding sequence causes maize salt sensitivity. We identified two ethyl methanesulfonate-induced mutants, zmsos1–1 and zmsos1–2 , which were severely sensitive to salt stress. Overexpression of ZmSOS1 enhanced maize seedling salt tolerance. ZmSOS1 can increase the salt tolerance of Arabidopsis sos1–1 mutant and can be activated by AtSOS2 and AtSOS 3 in yeast cells, suggesting that ZmSOS1 confers salt tolerance through the conserved SOS signaling pathway in maize, by promoting Na⁺ efflux from root cells and reducing shoot Na⁺ accumulation to maintain cellular ion homeostasis. The detrimental allele harboring the 4-bp deletion was rarely found in the natural population but appeared in an important heterotic group composed of x1132x-derived inbred lines which have been used widely for breeding dozens of hybrid varieties in China. The 4-bp deletion-based molecular marker has been successfully used to improve salt-sensitive varieties in a backcross and marker-assisted breeding program.